The majority of conventional antibiotics have been created for the treatment of planktonic bacteria. Antibiotic treatment of planktonic bacteria (not bacteria within a biofilm), has been the foremost application of microbiology research beginning with the advent of penicillin, until the modern characterization of biofilms in 1978. Clinically, the implications of biofilms are serious, as bacteria and fungi in biofilms exhibit tolerance to most clinically relevant pharmacokinetic/pharmacodynamic (PK/PD) dosing regimens of antimicrobials, in spite of susceptibility of the same pathogens as planktonic cells. Indeed, sub-minimal inhibitory concentrations of antimicrobials have been shown to induce biofilm formation, as a resistance and protection mechanism. When a bacterial or fungal cell switches to the biofilm mode of growth, it undertakes a phenotypic shift in its growth progression, with a large alteration in gene regulation. Therefore, there exists a need for methods and systems that can proactively reduce the risk of serious bacterial or fungal infections, by prophylactically inhibiting biofilm formation in microbes photo-biologically, so that after antimicrobials are given in/at a target site, without intolerable risks and/or intolerable adverse effects to human tissues where the pathogens are growing, the biofilm production is inhibited.